Only one health, and so many omics

Cancer Cell International

Marko Pećina¹  Nives Pećina-Šlaus² 

[1] Department of Medical Sciences Croatian Academy of Sciences and Arts, Zrinski trg 11, Zagreb, Croatia;Department of Biology, School of Medicine, University of Zagreb, Salata 3, Zagreb, Croatia

关键词: Cancer;    Microbiomics;    Metabolomics;    Epigenomics;    Proteomics;    Genomics;    Omics;   

Others  :  1219330
DOI  :  10.1186/s12935-015-0212-2

 received in 2015-01-26, accepted in 2015-06-02,  发布年份 2015

【 摘 要 】

The development of new approaches based on wide profiling methods in studying biological and medical systems is bringing large amounts of data on a daily basis.

The causes of complex diseases have been directed to the genome examination bringing formidable knowledge. We can study genome, but also proteome, exome, transcriptome, epigenome, metabolome, and newcomers too such as microbiome, connectome and exposome. The title of this editorial is paraphrasing the famous saying of Victor Schlichter from Buenos Aires children hospital in Argentina who said “How unfair! Only one health, and so many diseases”. Today there is indeed a whole lot of omics. We think that we are lucky to have all the omics possible, but we also wanted to stress the importance of future holistic approach in integrating the knowledge omics has rewarded us.

【 授权许可】

   
2015 Pecina-Slaus and Pecina.

【 参考文献 】

• [1]Karn T. High-Throughput Gene Expression and Mutation profiling: Current Methods and Future Perspectives. Breast Care. 2013; 8:401-6.
• [2]Hocquette JF. Where are we in genomics? J Physiol Pharmacol. 2005; 56 Suppl 3:37-70.
• [3]Matafora V, Bachi A, Capasso G. Genomics and proteomics: how long do we need to reach clinical results? Blood Purif. 2013; 36:7-11.
• [4]Hutchins JR. What’s that gene (or protein)? Online resources for exploring functions of genes, transcripts and proteins. Mol Biol Cell. 2014; 25:1187-201.
• [5]Marian AJ. Sequencing your genome: what does it mean? Methodist Debakey Cardiovasc J. 2014; 10:3-6.
• [6]Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloğlu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009; 106:19096-101.
• [7]Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009; 461:272-6.
• [8]Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011; 12:745-55.
• [9]Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirbi A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013; 369:1502-11.
• [10]Vishwanathan N, Le H, Le T, Hu WS. Advancing biopharmaceutical process science through transcriptome analysis. Curr Opin Biotechnol. 2014; 30C:113-9.
• [11]Benito E, Barco A. The Neuronal Activity-Driven Transcriptome. Mol Neurobiol 2014 Jun 17. doi: 10.1007/s12035-014-8772-z [Epub ahead of print]
• [12]Pfeifer GP, Hainaut P. Next-generation sequencing: emerging lessons on the origins of human cancer. Curr Opin Oncol. 2011; 23:62-8.
• [13]Bell DW. Our changing view of the genomic landscape of cancer. J Pathol. 2010; 220:231-43.
• [14]Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science. 2013; 339(6127):1546-58.
• [15]Liu Z, Zhang S. Toward a systematic understanding of cancers: a survey of the pan-cancer study. Front Genet. 2014; 5:194.
• [16]Ma CX, Ellis MJ. The cancer genome atlas: clinical applications for breast cancer. Oncology (Williston Park). 2013; 27:1263-9.
• [17]Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A et al.. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004; 91:355-8.
• [18]Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, Ultan McDermott U, Campbell PJ. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015; 43(Database issue):D805-11.
• [19]Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R et al.. A census of human cancer genes. Nat Rev Cancer. 2004; 4:177-83.
• [20]Pecina-Slaus N. Wnt signal transduction pathway and apoptosis: a review. Cancer Cell Int. 2010; 10:22.
• [21]Legrain P, Rain JC. Twenty years of protein interactions studies for biological functions deciphering. J Proteomics. 2014; 107:93-7.
• [22]Ghafourian S, Sekawi Z, Raftari M, Ali MS. Application of proteomics in lab diagnosis. Clin Lab. 2013; 59:465-74.
• [23]Zhang Y, Jiao J, Yang P, Lu H. Mass spectrometry-based N-glicoproteomics for cancer biomarker discovery. Clin Proteomics. 2014; 11:18. BioMed Central Full Text
• [24]Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, et al. The human proteome project: Current state and future direction. Mol Cell Proteomics 2011, 10 M111.009993. doi:. 10. 1074/mcp.M111.009993 webcite
• [25]Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B. Mass-spectrometry-based draft of the human proteome. Nature. 2014; 2014(509):582-7.
• [26]Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V et al.. A draft map of the human proteome. Nature. 2014; 509:575-81.
• [27]Han Y, Garcia BA. Combining genomic and proteomic approaches for epigenetics research. Epigenomics. 2013; 5:439-52.
• [28]Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF. RNA regulation of epigenetic processes. Bioessays. 2009; 31:51-9.
• [29]Tollervey JR, Lunyak VV. Epigenetics: judge, jury and executioner of stem cell fate. Epigenetics. 2012; 7:823-40.
• [30]Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature. 1983; 301:89-92.
• [31]Hattori N, Ushijima T. Compendium of aberrant DNA methylation and histone modifications in cancer. Biochem Biophys Res Commun. 2014; 455:3-9.
• [32]Knox SS. From ‘omics’ to complex disease: a systems biology approach to gene-environment interactions in cancer. Cancer Cell Int. 2010; 10:11.
• [33]Barrow TM, Michels KB. Epigenetic epidemiology of cancer. Biochem Biophys Res Commun. 2014; 455:70-83.
• [34]Brown M, Dunn WB, Ellis DI, Goodacre R, Handl J, Knowles JD, O’Hagan S, Spasić I, Kell DB. A metabolome pipeline: from concept to data to knowledge. Metabolomics. 2005; 1:39-51.
• [35]Nicholson JK, Lindon JC, Holmes E. ‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica. 1999; 29:1181-9.
• [36]Calabrò A, Gralka E, Luchinat C, Saccenti E, Tenori L: A Metabolomic Perspective on Coeliac Disease. Autoimmune Diseases 2014:756138. http://dx. doi.org/10.1155/2014/756138 webcite
• [37]Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A. HMDB 3.0–The Human Metabolome Database in. Nucleic Acids Res. 2013; 41(Database issue):D801-7.
• [38]Kacser H, Burns JA. The control of flux. Symp Soc Exp Biol. 1973; 27(4th):65-104.
• [39]Acerenza L, Cornish-Bowden A. Generalization of the double modulation metod for in situ determination of elasticities. Biochem J. 1997; 327:217-23.
• [40]Wheatley DN. On the vital importance of fluid movement in organisms and cells: a short historical note from Harvey to Coulson and beyond. Med Hypoth. 1999; 52:275-84.
• [41]Fievet JB, Dillmann C, de Vienne D. Systemic properties of metabolic networks lead to an epistasis-based model for heterosis. Theor Appl Genet. 2010; 120:463-73.
• [42]Acerenza L. Design of large metabolic responses. Constraints and sensitivity analysis. J Theor Biol. 2000; 207:265-82.
• [43]Wheatley DN, Clegg JS. What determines the basal metabolic rate of vertebrate cells in vivo? BioSystems. 1994; 32:83-92.
• [44]Wheatley DN. Diffusion, perfusion and the exclusion principles in the structural and functional organization of the living cell: reappraisal of the properties of the’ground substance. J Exp Biol. 2003; 206:1955-61.
• [45]Kacser H, Burns JA. The molecular basis of dominance. Genetics. 1981; 97:639-66.
• [46]Phadnis N, Fry JD. Widespread Correlations Between Dominance and Homozygous Effects of Mutations: Implications for Theories of Dominance. Genetics. 2005; 171:385-92.
• [47]Lion S, Gabriel F, Bost B, Fievet J, Dillmann C, de Vienne D. An extension to the metabolic control theory taking into account correlations between enzyme concentrations. Eur J Biochem. 2004; 271:4375-91.
• [48]Egert M, de Graaf AA, Smidt H, de Vos WM, Venema K. Beyond diversity: functional microbiomics of the human colon. Trends Microbiol. 2006; 14:86-91.
• [49]Rajendhran J, Gunasekaran P. Human Microbiomics. Indian J Microbiol. 2010; 50:109-12.
• [50]Knights D, Costello EK, Knight R. Supervised classifcation of human microbiota. FEMS Microbiol Rev. 2011; 35:343-59.
• [51]Statinkov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV. A comprehensive evaluation of multicategory classification methods for microbiomic data. Microbiome. 2013; 1:11. BioMed Central Full Text
• [52]Sporns O. The human connectome: origins and challenges. Neuroimage. 2013; 80:53-61.
• [53]Rappaport SM. Implications of the exposome for exposure science. J Expo Sci Environ Epidemiol. 2011; 21:5-9.
• [54]Wild CP. The exposome: from concept to utility. Int J Epidemiol. 2012; 41:24-32.
• [55]Wild CP, Scalbert A, Herceg Z. Measuring the exposome: a powerful basis for evaluating environmental exposures and cancer risk. Environ Mol Mutagen. 2013; 54:480-99.
• [56]Buck Louis G, Sundaram R: Exposome: Time for Transformative Research. Stat Med 2012, 31 (22), doi: 10.1002/sim. 5496
• [57]Pleil JD. Categorizing biomarkers of the human exposome and developing metrics for assessing environmental sustainability. J Toxicol Environ Health B Crit Rev. 2012; 15:264-80.
• [58]Vrijheid M, Slama R, Robinson O, Chatzi L, Coen M, van den Hazel P, Thomsen C, Wright J, Athersuch TJ, Avellana N, Basagaña X, Brochot C, Bucchini L, Bustamante M, Carracedo A, Casas M, Estivill X, Fairley L, van Gent D, Gonzalez JR, Granum B, Gražulevičienė R, Gutzkow KB, Julvez J, Keun HC, Kogevinas M, McEachan RR, Meltzer HM, Sabidó E, Schwarze PE, Siroux V, Sunyer J, Want EJ, Zeman F, Nieuwenhuijsen MJ. The Human Early-Life Exposome (HELIX): project rationale and design. Environ Health Perspect. 2014; 122:535-44.